GEO DataSets

(Submitter supplied) In this study, we use mRNA-Seq to characterize and compare the leukocyte transcriptomes of Holstein, Jersey, and Cholistani with respect to variations in sequence, expression, and splicing.

Organism:

Bos taurus; Bos indicus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15750 GPL17401

3 Samples

Download data: TXT

(Submitter supplied) Structural and functional impacts of copy number variations (CNVs) on livestock genomes are not yet well understood. In this study, we have identified 1853 CNV regions (CNVRs) using population-scale sequencing data generated from 75 cattle of 8 breeds (Holstein, Angus, Jersey, Limousin, Romagnola, Brahman, Gir and Nelore). Individual genome sequence coverage ranged from 4 to 30 fold, with a mean of 11.8 fold. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11314

25 Samples

Download data: BED, PAIR

(Submitter supplied) Resistance traits of parasitic infestation and diseases in bovine breeds display various unknown differences in the immune response indicating to be related to the host`s genomic background. We studied the differential gene expression of monocyte-derived macrophages (MDMs) stimulated or unstimulated with LPS in vitro, from two bovine breeds by RNA sequence methodology. MDMs were grown in supplemented RPMI medium for 11 days. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19172

16 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19150

32 Samples

Download data: TXT

(Submitter supplied) We report the results of MIRA-Seq based high-throughput profiling of the bovine dermal fibroblast methylome from two different breeds of cattle (n=4/breed) to determine the breed-dependent differences in methylation.

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19150

8 Samples

Download data: TXT

(Submitter supplied) We report the breed-dependent differences in the innate immune response of dermal fibroblasts following exposure to lipopolysaccharide (LPS). Skin biopsies were collected from Angus (a beef breed) and Holstein (a dairy breed) animals and isolated fibroblasts were exposed to LPS to investigate differences in gene expression between these two cattle breeds.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19150

24 Samples

Download data: TXT

(Submitter supplied) The study investigated gene expression patterns in liver tissue to understand the biological functions of genes that are potentially involved in controlling / regulating feed efficiency in Nordic dairy cattle.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19172

38 Samples

Download data: TXT

(Submitter supplied) Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1,265 CNV regions comprising ~55.6 Mbp sequence-476 of which (~38%) have not previously been reported. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11314

5 Samples

Download data: PAIR, TXT

(Submitter supplied) We reported the bovine liver gene expression database of Polish-HF, Polish-Red and Hereford cattle breeds.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24980

18 Samples

Download data: ZIP

(Submitter supplied) Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, 3 Bos indicus and 3 composite breeds for beef, dairy or dual purpose. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL9865 GPL9866

90 Samples

Download data: PAIR, TXT